Without reading over everything that's been said...
My first thought was - I'm not sure it would be a good thing because, inevitably, Link would become very sexualized - as in, tight, tight tunic... maybe even a chainmail bra like on badly-done fantasy book covers. No, just no. As many girl gamers exist (myself included), videogames are thought of as mostly a "male hobby" to this day. It's beginning to change, but it seems that most games do things to appeal to the male gaze, if you know what I mean.
Some "equal opportunity" has happened - for example, I think Nintendo knows that Zelda has lots of (straight) female fans - Twilight Princess did the fanservice thing with the Sumo wrestling and Link's nicely-toned rancher's body. (Of course they did the funny by an immediate shot to Mayor Bo)... Still it was only one little scene/mini-game thing.
If he were a she... I worry that she'd be running around in an armor bra and panties the *whole freaking game.*
As much as I'd like to see more strong female protagonists (in any media), I think the videogame culture needs to get over the female objectification things first. Go back to the bulky suits and genreally practical clothing - just because the hero is a lady doesn't mean she has to show every last curve.
And, I'm just used to Link as a boy/man. I read somewhere - in regards to sexism in modern literature, that stories with male protagonists often do better (and get agents/publishers inerested in books) better ones with female protagonists because the way culture (Western or just world?) grooms us with the idea of male heroes. As a result, according to the article, girls can easily identify with male protagonists despite the gender much better than males can identify with a female. - As I recall, the gist of the article was basically something like "If J.K. Rowling had created a Harriet Potter, she never would have sold a book."
That said, I seem to enjoy writing female protagonists in my own, original books, but when it comes to fanfiction/roleplay of pop culture/already existant stuff, I tend to find myself "identifying" best with male heroes for some reason.
I need to finish playing Metroid Prime.